Specific protein-RNA interactions are mostly preserved in biomolecular condensates
Many biomolecular condensates are enriched in and depend on RNAs and RNA binding proteins (RBPs). So far, only a few studies have addressed the characterization of the intermolecular interactions responsible for liquid-liquid phase separation (LLPS) and the impact of condensation on RBPs and RNAs. H...
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| Veröffentlicht in: | Science advances 2024-03, Vol.10 (10), p.eadm7435-eadm7435 |
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| creator | de Vries, Tebbe Novakovic, Mihajlo Ni, Yinan Smok, Izabela Inghelram, Clara Bikaki, Maria Sarnowski, Chris P Han, Yaning Emmanouilidis, Leonidas Padroni, Giacomo Leitner, Alexander Allain, Frédéric H-T |
| description | Many biomolecular condensates are enriched in and depend on RNAs and RNA binding proteins (RBPs). So far, only a few studies have addressed the characterization of the intermolecular interactions responsible for liquid-liquid phase separation (LLPS) and the impact of condensation on RBPs and RNAs. Here, we present an approach to study protein-RNA interactions inside biomolecular condensates by applying cross-linking of isotope labeled RNA and tandem mass spectrometry to phase-separating systems (LLPS-CLIR-MS). LLPS-CLIR-MS enables the characterization of intermolecular interactions present within biomolecular condensates at residue-specific resolution and allows a comparison with the same complexes in the dispersed phase. We observe that sequence-specific RBP-RNA interactions present in the dispersed phase are generally maintained inside condensates. In addition, LLPS-CLIR-MS identifies structural alterations at the protein-RNA interfaces, including additional unspecific contacts in the condensed phase. Our approach offers a procedure to derive structural information of protein-RNA complexes within biomolecular condensates that could be critical for integrative structural modeling of ribonucleoproteins (RNPs) in this form. |
| doi_str_mv | 10.1126/sciadv.adm7435 |
| format | Article |
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So far, only a few studies have addressed the characterization of the intermolecular interactions responsible for liquid-liquid phase separation (LLPS) and the impact of condensation on RBPs and RNAs. Here, we present an approach to study protein-RNA interactions inside biomolecular condensates by applying cross-linking of isotope labeled RNA and tandem mass spectrometry to phase-separating systems (LLPS-CLIR-MS). LLPS-CLIR-MS enables the characterization of intermolecular interactions present within biomolecular condensates at residue-specific resolution and allows a comparison with the same complexes in the dispersed phase. We observe that sequence-specific RBP-RNA interactions present in the dispersed phase are generally maintained inside condensates. In addition, LLPS-CLIR-MS identifies structural alterations at the protein-RNA interfaces, including additional unspecific contacts in the condensed phase. Our approach offers a procedure to derive structural information of protein-RNA complexes within biomolecular condensates that could be critical for integrative structural modeling of ribonucleoproteins (RNPs) in this form.</description><identifier>ISSN: 2375-2548</identifier><identifier>EISSN: 2375-2548</identifier><identifier>DOI: 10.1126/sciadv.adm7435</identifier><identifier>PMID: 38446881</identifier><language>eng</language><publisher>United States: American Association for the Advancement of Science</publisher><subject>Biochemistry ; Biomedicine and Life Sciences ; Life Sciences ; SciAdv r-articles</subject><ispartof>Science advances, 2024-03, Vol.10 (10), p.eadm7435-eadm7435</ispartof><rights>Copyright © 2024 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution License 4.0 (CC BY). 2024 The Authors</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c346t-8e573ecea204455048331577861dea9a4503d363ec61058766f8857c380b9a403</cites><orcidid>0000-0001-8851-3537 ; 0000-0002-9649-5620 ; 0009-0007-2568-6044 ; 0000-0001-7654-9663 ; 0009-0007-5066-6256 ; 0009-0000-3282-2699 ; 0000-0002-2131-6237 ; 0000-0002-1406-4449 ; 0000-0003-4126-0725 ; 0009-0007-9056-1045</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC10917357/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC10917357/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,27901,27902,53766,53768</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/38446881$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>de Vries, Tebbe</creatorcontrib><creatorcontrib>Novakovic, Mihajlo</creatorcontrib><creatorcontrib>Ni, Yinan</creatorcontrib><creatorcontrib>Smok, Izabela</creatorcontrib><creatorcontrib>Inghelram, Clara</creatorcontrib><creatorcontrib>Bikaki, Maria</creatorcontrib><creatorcontrib>Sarnowski, Chris P</creatorcontrib><creatorcontrib>Han, Yaning</creatorcontrib><creatorcontrib>Emmanouilidis, Leonidas</creatorcontrib><creatorcontrib>Padroni, Giacomo</creatorcontrib><creatorcontrib>Leitner, Alexander</creatorcontrib><creatorcontrib>Allain, Frédéric H-T</creatorcontrib><title>Specific protein-RNA interactions are mostly preserved in biomolecular condensates</title><title>Science advances</title><addtitle>Sci Adv</addtitle><description>Many biomolecular condensates are enriched in and depend on RNAs and RNA binding proteins (RBPs). So far, only a few studies have addressed the characterization of the intermolecular interactions responsible for liquid-liquid phase separation (LLPS) and the impact of condensation on RBPs and RNAs. Here, we present an approach to study protein-RNA interactions inside biomolecular condensates by applying cross-linking of isotope labeled RNA and tandem mass spectrometry to phase-separating systems (LLPS-CLIR-MS). LLPS-CLIR-MS enables the characterization of intermolecular interactions present within biomolecular condensates at residue-specific resolution and allows a comparison with the same complexes in the dispersed phase. We observe that sequence-specific RBP-RNA interactions present in the dispersed phase are generally maintained inside condensates. In addition, LLPS-CLIR-MS identifies structural alterations at the protein-RNA interfaces, including additional unspecific contacts in the condensed phase. 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| source | DOAJ Directory of Open Access Journals; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; PubMed Central |
| subjects | Biochemistry Biomedicine and Life Sciences Life Sciences SciAdv r-articles |
| title | Specific protein-RNA interactions are mostly preserved in biomolecular condensates |
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